The Free Energy Landscape Analysis of Protein (FIP35) Folding Dynamics

2011 ◽  
Vol 115 (42) ◽  
pp. 12315-12324 ◽  
Author(s):  
Sergei V. Krivov
Keyword(s):  
Free Energy ◽  
Energy Landscape ◽  
Landscape Analysis ◽  
Free Energy Landscape ◽  
Folding Dynamics

High-resolution free energy landscape analysis of protein folding

2015 ◽  
Vol 43 (2) ◽  
pp. 157-161 ◽  
Author(s):  
Polina V. Banushkina ◽  
Sergei V. Krivov
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
High Resolution ◽  
Energy Landscape ◽  
Quantitative Description ◽  
Free Energy Landscape ◽  
Transition Path ◽  
Exponential Factor ◽  
Basic Properties ◽  
Folding Dynamics

The free energy landscape can provide a quantitative description of folding dynamics, if determined as a function of an optimally chosen reaction coordinate. The profile together with the optimal coordinate allows one to directly determine such basic properties of folding dynamics as the configurations of the minima and transition states, the heights of the barriers, the value of the pre-exponential factor and its relation to the transition path times. In the present study, we review the framework, in particular, the approach to determine such an optimal coordinate, and its application to the analysis of simulated protein folding dynamics.

Conformational modifications induced by internal tandem duplications on the FLT3 kinase and juxtamembrane domains

2019 ◽  
Vol 21 (34) ◽  
pp. 18467-18476 ◽  
Author(s):  
Guido Todde ◽  
Ran Friedman
Keyword(s):  
Free Energy ◽  
Protein Kinase ◽  
Molecular Dynamic ◽  
Energy Landscape ◽  
Landscape Analysis ◽  
Free Energy Landscape ◽  
Molecular Dynamic Simulations ◽  
Dynamic Simulations ◽  
Tandem Duplications

FLT3 is a protein kinase that becomes aberrantly expressed in certain leukaemias. Insertions in the form of tandem duplications activate the protein and were studied by molecular dynamic simulations and free energy landscape analysis.

scholarly journals Free Energy Landscape Analysis System Based on Parallel Molecular Dynamics Simulation

2007 ◽  
Vol 3 ◽  
pp. 757-766
Author(s):  
Masakazu Sekijima ◽  
Jun Doi ◽  
Shinya Honda ◽  
Tamotsu Noguchi ◽  
Shigenori Shimizu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Energy Landscape ◽  
Landscape Analysis ◽  
Dynamics Simulation ◽  
Free Energy Landscape ◽  
Parallel Molecular Dynamics ◽  
Analysis System
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